Strong Linkage Disequilibrium and Proxy Effect of <i>PPP1R16A</i> rs109146371 for <i>DGAT1</i> K232A in Japanese Holstein Cattle.

ABSTRACT:

Background/objectives

DGAT1 p. K232A (rs109234250) is a well-established causal variant influencing milk fat and protein content in dairy cattle, but it is often absent from commercial genotyping arrays. PPP1R16A rs109146371 frequently appears as a top signal in genome-wide association studies (GWAS) for milk traits. This study aimed to evaluate the linkage disequilibrium (LD) between these two variants in Japanese Holsteins and assess whether rs109146371 exerts an independent effect on milk traits.

Methods

A total of 256 Japanese Holstein cows were genotyped for DGAT1 p. K232A and PPP1R16A rs109146371 using TaqMan SNP assays. LD statistics (r², D') were computed, and linear mixed-effects models were used to evaluate associations with 305-day milk yield, fat percentage, protein percentage, and solids-not-fat (SNF) percentage. Likelihood ratio tests were conducted to assess the independence of SNP effects.

Results

Strong LD was observed between DGAT1 p. K232A and PPP1R16A rs109146371 (r² = 0.91, D' = 0.9962). Both SNPs showed significant associations with all milk production traits; however, model comparisons indicated that rs109146371 did not improve model fit when K232A was included, suggesting no independent effect.

Conclusions

PPP1R16A rs109146371 serves as a proxy for DGAT1 K232A rather than an independent determinant of milk traits.

SUBMITTER: Akiyama Y 

PROVIDER: S-EPMC12469489 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature